Greater White-fronted Goose Anser albifrons has a holarctic breeding distribution and is polymorphic. Three subspecies winter in the Palaearctic region, one of which also winters in the Nearctic region: European White-fronted Goose A. a. albifrons breeds in the far north of Europe and Asia and winters in the south and west of Europe; Pacific White-fronted Goose A. a. frontalis breeds in east Siberia and Arctic Canada and winters in East Asia and United States; and Greenland White-fronted Goose A. a. flavirostris breeds in Greenland and winters in Ireland and western Scotland. The phylogenetic relationships among these three subspecies are unclear. We determined the mitochondrial DNA control region sequences of Pacific Whitefronted Goose, using 66 shed feathers collected from wintering sites in Japan, and compared the sequences with those previously published for Greater White-fronted Goose subspecies. Phylogenetic trees and networks revealed that there are three clades within the species. The sequence divergence among the clades corresponds to divergence long before the last glacial maximum (15–25 thousand years ago), which suggests the existence of at least three ancient refugia for the species. However, all three subspecies consist of haplotypes from two of the three clades. This suggests that they originated from individuals that survived in two refugia during the last glacial period.